Variant report

Variant	rs1598865
Chromosome Location	chr6:77500526-77500527
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10455322	1.00[AFR][1000 genomes]
rs11969816	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12174426	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12191933	1.00[AFR][1000 genomes]
rs12192489	1.00[AFR][1000 genomes]
rs12660959	0.98[ASN][1000 genomes]
rs12661295	1.00[AFR][1000 genomes]
rs13211725	1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1335436	1.00[AFR][1000 genomes]
rs1350404	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1350941	0.97[ASN][1000 genomes]
rs1414184	1.00[AFR][1000 genomes]
rs1462469	1.00[AFR][1000 genomes]
rs1570260	1.00[AFR][1000 genomes]
rs1598866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1981128	1.00[AFR][1000 genomes]
rs34264360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35236070	1.00[AFR][1000 genomes]
rs35512517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35822653	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs68040563	1.00[AFR][1000 genomes]
rs68139108	1.00[AFR][1000 genomes]
rs68172709	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs71563003	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9341621	1.00[AFR][1000 genomes]
rs9343499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9343507	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9343513	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9350675	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9350677	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9350684	1.00[AFR][1000 genomes]
rs9352390	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9352400	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9352403	1.00[AFR][1000 genomes]
rs9359223	1.00[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs9359230	1.00[AFR][1000 genomes]
rs9361140	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9361152	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9361153	0.95[ASN][1000 genomes]
rs9361156	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9361157	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9361162	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019520	chr6:77355212-77875164	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv538321	chr6:77355212-77875164	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv886218	chr6:77415155-77500526	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv886220	chr6:77415155-77505717	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv886219	chr6:77415155-77515516	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1598865	SLC17A5	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:77499000-77501600	Enhancers	Fetal Intestine Large	intestine
2	chr6:77499200-77501000	Enhancers	Duodenum Mucosa	Duodenum
3	chr6:77499200-77501000	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr6:77499600-77530800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:77499800-77500600	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr6:77499800-77500800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:77500000-77500800	Enhancers	Stomach Mucosa	stomach
8	chr6:77500000-77501000	Enhancers	HepG2	liver
9	chr6:77500200-77500800	Weak transcription	Pancreas	Pancrea
10	chr6:77500200-77501200	Enhancers	Liver	Liver
11	chr6:77500400-77501400	Enhancers	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links